-rw-r--r-- | analysis/year.R | 20 | ||||
-rw-r--r-- | src/Makefile.am | 39 | ||||
-rw-r--r-- | src/aggregator.c | 6 | ||||
-rw-r--r-- | src/assign/assign_protein_type.c (renamed from src/assign_protein_type.c) | 87 | ||||
-rw-r--r-- | src/assign/assign_protein_type.h (renamed from src/assign_protein_type.h) | 0 | ||||
-rw-r--r-- | src/error/check_error.c (renamed from src/check_error.c) | 0 | ||||
-rw-r--r-- | src/error/check_error.h (renamed from src/check_error.h) | 0 | ||||
-rw-r--r-- | src/error/check_h5_error.c (renamed from src/check_h5_error.c) | 0 | ||||
-rw-r--r-- | src/error/check_h5_error.h (renamed from src/check_h5_error.h) | 0 | ||||
-rw-r--r-- | src/error/check_ncbi_error.c (renamed from src/check_ncbi_error.c) | 0 | ||||
-rw-r--r-- | src/error/check_ncbi_error.h (renamed from src/check_ncbi_error.h) | 0 | ||||
-rw-r--r-- | src/load/load_influenza_aa_dat.c (renamed from src/load_influenza_aa_dat.c) | 4 | ||||
-rw-r--r-- | src/load/load_influenza_aa_dat.h (renamed from src/load_influenza_aa_dat.h) | 0 | ||||
-rw-r--r-- | src/load/load_influenza_faa.c (renamed from src/load_influenza_faa.c) | 10 | ||||
-rw-r--r-- | src/load/load_influenza_faa.h (renamed from src/load_influenza_faa.h) | 0 | ||||
-rw-r--r-- | src/model/gi_type_data.h | 21 | ||||
-rw-r--r-- | src/model/gi_type_data_init.c | 36 | ||||
-rw-r--r-- | src/model/gi_type_data_init.h | 14 | ||||
-rw-r--r-- | src/model/sequence_data.h (renamed from src/sequence_data.h) | 5 | ||||
-rw-r--r-- | src/model/sequence_data_init.c (renamed from src/sequence_data_init.c) | 6 | ||||
-rw-r--r-- | src/model/sequence_data_init.h (renamed from src/sequence_data_init.h) | 0 | ||||
-rw-r--r-- | src/updator.c | 4 |
22 files changed, 181 insertions, 71 deletions
diff --git a/src/load/load_influenza_faa.c b/src/load/load_influenza_faa.c new file mode 100644 index 0000000..a217989 --- a/dev/null +++ b/src/load/load_influenza_faa.c | |||
@@ -0,0 +1,97 @@ | |||
1 | #include "error/check_error.h" | ||
2 | #include "error/check_h5_error.h" | ||
3 | #include "load_influenza_faa.h" | ||
4 | #include "model/sequence_data.h" | ||
5 | #include "model/sequence_data_init.h" | ||
6 | #include <hdf5_hl.h> | ||
7 | #include <string.h> | ||
8 | #include <stdlib.h> | ||
9 | |||
10 | void | ||
11 | load_influenza_faa (hid_t file_id) | ||
12 | { | ||
13 | size_t dst_size; | ||
14 | size_t dst_offset[SEQUENCE_DATA_FIELD_NUM]; | ||
15 | size_t dst_sizes[SEQUENCE_DATA_FIELD_NUM]; | ||
16 | hid_t field_type[SEQUENCE_DATA_FIELD_NUM]; | ||
17 | |||
18 | sequence_data_init (&dst_size, dst_offset, dst_sizes, field_type); | ||
19 | |||
20 | hsize_t chunk_size = 10; | ||
21 | int *fill_data = NULL; | ||
22 | int compress = 0; | ||
23 | |||
24 | sequence_data p_data; | ||
25 | FILE *dat = fopen ("/home/don/exp004/genomes/INFLUENZA/influenza.faa", | ||
26 | "r"); | ||
27 | if (dat == NULL) | ||
28 | check_error (__FILE__, __LINE__); | ||
29 | char *line = NULL; | ||
30 | size_t len = 0; | ||
31 | int current_line = 0; | ||
32 | |||
33 | while (getline (&line, &len, dat) != -1) | ||
34 | { | ||
35 | current_line++; | ||
36 | |||
37 | // Header line. | ||
38 | if (line[0] == '>') | ||
39 | { | ||
40 | char *running = strdup (line); | ||
41 | char *token = NULL; | ||
42 | |||
43 | // Eat the ">gi". | ||
44 | strsep (&running, "|"); | ||
45 | |||
46 | // GI value. | ||
47 | token = strsep (&running, "|"); | ||
48 | p_data.gi = atoi (token); | ||
49 | |||
50 | // Eat the "gb" | ||
51 | strsep (&running, "|"); | ||
52 | |||
53 | // GB value. | ||
54 | strncpy (p_data.gb, strsep(&running, "|"), sizeof (p_data.gb)); | ||
55 | |||
56 | // Description value. | ||
57 | strncpy (p_data.description, strsep (&running, "|"), | ||
58 | sizeof (p_data.description)); | ||
59 | |||
60 | const char* sequence_data_field_names[SEQUENCE_DATA_FIELD_NUM] = | ||
61 | SEQUENCE_DATA_FIELD_NAMES; | ||
62 | |||
63 | if (current_line == 1) | ||
64 | { | ||
65 | herr_t status = H5TBmake_table ("influenza.faa", file_id, | ||
66 | "influenza.faa", | ||
67 | SEQUENCE_DATA_FIELD_NUM, 1, | ||
68 | dst_size, sequence_data_field_names, | ||
69 | dst_offset, field_type, | ||
70 | chunk_size, fill_data, compress, | ||
71 | &p_data); | ||
72 | if (status < 0) | ||
73 | check_h5_error (status, __FILE__, __LINE__); | ||
74 | } | ||
75 | else | ||
76 | { | ||
77 | herr_t status = | ||
78 | H5TBappend_records (file_id, "influenza.faa", 1, dst_size, | ||
79 | dst_offset, dst_sizes, &p_data); | ||
80 | if (status < 0) | ||
81 | check_h5_error (status, __FILE__, __LINE__); | ||
82 | } | ||
83 | |||
84 | if (running) | ||
85 | free (running); | ||
86 | |||
87 | } | ||
88 | |||
89 | } | ||
90 | |||
91 | if (line) | ||
92 | free (line); | ||
93 | |||
94 | fclose (dat); | ||
95 | |||
96 | return; | ||
97 | } | ||